Intercalation is one of several modes by which drugs interact with DNA wherein a planar portion of the drug is inserted in between adjacent stacked base pairs of a double stranded DNA. The intercalation process results in helix extension and unwinding of the DNA. Included within these drugs are antitumor agents, actinomycin D, adriamycin and daunomycin, as well as several drugs for treatment of parasitic disease including ethidium bromide, quinacrine, chloroquine and miracil D. U.S. Pat. No. 2,441,665 discloses a class of alkylene diamine derivatives which are valuable as antimalarial agents. U.S. Pat. No. 2,113,357 discloses substituted amino-acridine derivatives useful in treating blood parasites.
DNA intercalating ligands have also been shown to be useful in targeting alkylating agents to DNA by attachment of the intercalating ligand to the alkylating agent (Gourdie, et al. (1991) J. Med. Chem. 34:240-248). Since the biological properties of these DNA intercalating drugs are believed to result from their binding, research efforts have focused on designing molecules that have a high affinity for DNA. Planar polycyclic aromatic molecules show a strong propensity to bind to DNA by intercalation (Jaycox, et al. (1987) J. Heterocyclic Chem. 24:1405-1408; U.S. Pat. No. 6,187,787). In this respect, efforts to identify molecules with a greater affinity and selectivity for DNA have resulted in the development of bifunctional intercalating agents in which two intercalating ligands are bridged by a central linking chain. In general, enhanced binding is observed with molecules of this type (Canellakis, et al. (1976) Biochim. Biophys. Acta 418:277; Becker & Dervan (1979) J. Am. Chem. Soc. 101:3664; Wakelin, et al. (1986) Med. Res. Rev. 6:275).
A homologous series of bisacridines containing two 9-aminoacridine chromophores linked via a simple methylene chain has been studied to investigate the minimum interchromophore separation required to permit bifunctional intercalation (Wakelin, et al. (1978) Biochemistry 17:5057). Viscometric, sedimentation and electric dichroism experiments showed that compounds having one to four methylene groups in the linker are restricted to monofunctional intercalation whereas bifunctional interaction was observed when the chain length was increased to six methylene groups or more.
Additional studies indicate that the nature of the bridging chain and/or substituents on the acridine ring has a profound effect on the ability of bisacridine compounds to act as bifunctional intercalating agents. DNA binding characteristics of a number of acridine dimers of which two aromatic rings, each ring being the monomeric 2-methoxy-6-chloro-9-(3-dimethyl amino propylamino acridine), were linked by a chain of varying length and structure were also determined (Le Pecq, et al. (1975) Proc. Nat'l Acad. Sci. USA 72(8):2915-2919). The linking chains of these acridine dimers included —(CH2)3—NH—(CH2)4—NH—(CH2)3—; —(CH2)3—NH—(CH2)4—; and —(CH2)3—NH—(CH2)3—. It was found that the two dimers with the longest chain length bis-intercalated, while only one of the two rings of the dimer with the shortest chain was intercalated. In contrast, bis-intercalators bridged by flexible chains have generally exhibited reduced affinities for DNA, in part because of self-stacking interactions, which compete with the binding process (Barbet, et al. (1976) Biochemistry 15:2642; Capelle, et al. (1979) Biochemistry 18:3354). Further, bis-intercalation can introduce undesirable entropic effects when a flexible linker is forced into an extended chain conformation (Jaycox et al. (1987) supra). In addition, it is a concern that flexible bis-intercalators can creep in a step-wise fashion along the DNA macromolecule, thereby lowering ligand residence lifetimes at any one site (Denny, et al. (1985) J. Med. Chem. 28:1568). Such a process could have significant effects on efficacy of these intercalators as anticancer agents as residence lifetimes have been correlated with in vivo antitumor activity for a large number of DNA intercalators (Feigon, et al. (1984) J. Med. Chem. 27:450).